7W7L

Structure of NF-kB p52 homodimer bound to 13-mer A/T-centric P-Selectin kB DNA fragment

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1A3Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293	50mM MES, pH 6.0, 10mM MgCl2, 10% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
4.36	71.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 225.276	α = 90
b = 225.276	β = 90
c = 96.937	γ = 120

Symmetry
Space Group	P 62 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M		2019-11-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U1	0.979183	SSRF	BL17U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	3	48.77	100	0.999	18	37.3		29500

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3	3.16			0.84	2.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1A3Q	3	48.77	29472	1529	99.929	0.239	0.2376	0.2581	116.662

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
1.94	0.97		1.94		-6.294

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.45
r_lrange_it	19.404
r_lrange_other	19.404
r_dihedral_angle_3_deg	18.997
r_dihedral_angle_4_deg	16.592
r_mcangle_it	13.925
r_mcangle_other	13.924
r_scangle_it	11.676
r_scangle_other	11.675
r_mcbond_it	9.118
r_mcbond_other	9.113
r_dihedral_angle_1_deg	7.661
r_scbond_it	7.445
r_scbond_other	7.444
r_angle_refined_deg	1.887
r_angle_other_deg	1.395
r_symmetry_xyhbond_nbd_refined	0.268
r_symmetry_nbd_other	0.22
r_nbd_refined	0.213
r_ncsr_local_group_1	0.205
r_nbtor_refined	0.185
r_xyhbond_nbd_refined	0.165
r_symmetry_xyhbond_nbd_other	0.143
r_nbd_other	0.14
r_symmetry_nbd_refined	0.123
r_chiral_restr	0.122
r_ext_dist_refined_d	0.095
r_symmetry_nbtor_other	0.088
r_ncsr_local_group_2	0.074
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4640
Nucleic Acid Atoms	527
Solvent Atoms	24
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing